The long-term objective of this portion of the Program Project Grant with Johns Hopkins is to develop high-speed, massively parallel capillary array electrophoresis apparatus and methods that can be used for efficient multiplex analysis of cancer genotypes. These studies will provide technologies that can be used for cancer diagnostic applications and will lead to the identification of specific gene alterations associated with cancer development. Initially, a capillary array scanner capable of performing up to 1024 DNA amplicon electrophoretic separations in under 1 hour will be constructed, evaluated and optimized at Berkeley. A scientist from John Hopkins will work at Berkeley to aid in the optimization of this apparatus and to learn how to run the apparatus and analyze these data. Then this apparatus will be moved to John Hopkins where it will be used in cancer genotyping studies. The initial system will be operated at 1/4 capacity loading 256 samples. It will be upgraded to lead and run up to 1024 capillaries as more samples and ET primers become available. Custom ET primers will be synthesized throughout this work by a technician at Berkeley. In a parallel effort, a graduate student will work at Berkeley on the microfabrication of capillary array electrophoresis systems on 4" glass wafers and on the development of chip scanners. These capillary array electrophoresis microplates will be designed to run 96 samples and to perform separation that are 10-times faster than the conventional capillary array apparatus mentioned above. Samples will be loaded on the chips with multihead pipetters and detection will be provided with custom chip scanners. If these chips are successful, a chip scanner and chips will be provided to Johns Hopkins for evaluation in cancer genotyping studies in the third year of this grant. The CAE microplates should be particularly valuable for real-time analysis of samples taken during surgery to evaluate tumor progression and to provide the next generation in inexpensive fast and high through-put cancer genotyping and diagnostic devices.